The only thing BYU would confirm about Brandon Davies suspension was that his Honor Code violation was not a criminal offense. However, the reason eventually did come out and according to the Salt Lake Tribune it was because Davies had sex with his girlfriend. Having sex before marriage is against the Honor Code and is against the LDS faith in general. This is the exact same thing that force former BYU running back Harvey Unga out of school last year.
Davies is still enrolled at BYU, but that status is still to be determined as is his status with the team for next season. The difference between Davies and Unga is that Unga's offense was his second offense for the the exact same thing. As for what has been released about Davies this is his only Honor Code offense, so Davies outcome might be different then Unga's.
All that will be said about the Honor Code is that the players and students at BYU know what they are getting to when the attend BYU and agree to follow the rules, and while young college age kids do make mistakes Davies was full aware of the consequences if he broke the Honor Code.